For alignment and scaling purposes, it is necessary to place some reference marks on the surface of the pumpkin. I applied masking tape, onto which I drew small crosses. Looking back at it, I ended up spending a fair amount of time trying to align the mesh in CAD and trying to align the actual pumpkin on the machine bed. By adding more reference marks at the beginning, the alignment at later stages would have been easier and more accurate.
In terms of taking pictures for use in 123D Catch, I would like to give a little bit of advice. First of all, don't bother spending lots of time building contraptions to automate the picture taking process. I know there are some plans published all over the internet, but I think your time is more wisely spent by studying and understanding the excellent tutorials on the 123D website: http://www.123dapp.com/catch/learn
Catch is very capable and as long as you follow the advice in the tutorials, very good results can be achieved by just using a hand held camera on it's own. One thing I noticed is that a lot of peoples, also some of the guys (m/f) with the automatic-picture-taking devices, only take a series of picture in a circle at a single
elevation. The best results, as advised in the tutorials, is achieved by taking pictures at two elevations.